Greg,
Thank you for the explanation. I guess my main concern now is how to
depict this. When I try to depict it in 2D, the isotope (e.g. 13) is
not depicted to the upper left of C. Is the RDKit drawing functionality
able to depict isotopes in the drawings?
Thanks
Don
On 06/15/2011 12:02 AM, Greg Landrum wrote:
> The isotope property is read and the mass of the atom is adjusted:
> [3]>>> m = Chem.MolFromMolFile('iso.mol')
>
> [4]>>> m.GetAtomWithIdx(0).GetMass()
> Out[4] 13.0
>
> There's not currently a way to find out directly if the isotope of an
> atom has been set; I hope to have this fixed for the next release, but
> I'm not yet sure that's going to happen.
>
> As an FYI, when the RDKit generates mol blocks, it currently puts the
> isotope information in the atom line, not in an M ISO line:
>
> [5]>>> print Chem.MolToMolBlock(m)
> -----> print(Chem.MolToMolBlock(m))
> Benzene-13C1
> RDKit 2D
>
> 6 6 0 0 0 0 0 0 0 0999 V2000
> 0.0000 0.8250 0.0000 C 1 0 0 0 0 0 0 0 0 0 0 0
> -0.7145 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.7145 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.0000 -0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.7145 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.7145 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1 2 2 0
> 6 1 1 0
> 2 3 1 0
> 3 4 2 0
> 4 5 1 0
> 5 6 2 0
> M END
>
> I will definitely get this updated for the next release.
>
> -greg
>
>
> On Wed, Jun 15, 2011 at 12:07 AM, Donald Keidel<[email protected]>
> wrote:
>> Hi,
>>
>> I am reading an sd file that has an M ISO line (carbon 13 isotope).
>> Here is the sd file:
>>
>> Benzene-13C1
>> OpenBabl03260920282D
>>
>> 6 6 0 0 0 0 0 0 0 0999 V2000
>> 0.0000 0.8250 0.0000 C 0 0 0 0 0
>> -0.7145 0.4125 0.0000 C 0 0 0 0 0
>> -0.7145 -0.4125 0.0000 C 0 0 0 0 0
>> 0.0000 -0.8250 0.0000 C 0 0 0 0 0
>> 0.7145 -0.4125 0.0000 C 0 0 0 0 0
>> 0.7145 0.4125 0.0000 C 0 0 0 0 0
>> 1 2 2 0 0 0
>> 6 1 1 0 0 0
>> 2 3 1 0 0 0
>> 3 4 2 0 0 0
>> 4 5 1 0 0 0
>> 5 6 2 0 0 0
>> M ISO 1 1 13
>> M END
>>
>> I then try to display the properties of atom 1 (0 in RDKit since zero
>> based lists) and this is what I see:
>>
>> I read the mol
>> .
>> .
>> .
>> .
>> >>> mol
>> <rdkit.Chem.rdchem.Mol object at 0x1d21a60>
>> >>> atom = mol.GetAtoms()[0]
>> >>> prop = atom.GetPropNames()[0]
>> Traceback (most recent call last):
>> File "<stdin>", line 1, in<module>
>> IndexError: Index out of range
>>
>>
>> Isnt the ISO property supposed to be read as a property of the atom? Am
>> I doing something wrong or interpreting something incorrectly?
>>
>> Thank you in advance for any help.
>>
>> Don
>>
>>
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